help please with minimap2, tabix, bgzip and bcftools binary files

[davidmadariaga]

hi, i installed medaka with pip, following the instructions described in the main page. i already installed all required programs but medakat still does not recognize those binary files. This is my .bashrc file:

"# ~/.bashrc: executed by bash(1) for non-login shells.

see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)

for examples

If not running interactively, don't do anything

case $- in i) ;; *) return;; esac

don't put duplicate lines or lines starting with space in the history.

See bash(1) for more options

HISTCONTROL=ignoreboth

append to the history file, don't overwrite it

shopt -s histappend

for setting history length see HISTSIZE and HISTFILESIZE in bash(1)

HISTSIZE=1000 HISTFILESIZE=2000

check the window size after each command and, if necessary,

update the values of LINES and COLUMNS.

shopt -s checkwinsize

If set, the pattern "**" used in a pathname expansion context will

match all files and zero or more directories and subdirectories.

shopt -s globstar

make less more friendly for non-text input files, see lesspipe(1)

[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"

set variable identifying the chroot you work in (used in the prompt below)

if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then debian_chroot=$(cat /etc/debian_chroot) fi

set a fancy prompt (non-color, unless we know we "want" color)

case "$TERM" in xterm-color|*-256color) color_prompt=yes;; esac

uncomment for a colored prompt, if the terminal has the capability; turned

off by default to not distract the user: the focus in a terminal window

should be on the output of commands, not on the prompt

force_color_prompt=yes

if [ -n "$force_color_prompt" ]; then if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then

We have color support; assume it's compliant with Ecma-48

# (ISO/IEC-6429). (Lack of such support is extremely rare, and such
# a case would tend to support setf rather than setaf.)
color_prompt=yes
else
color_prompt=
fi

fi

if [ "$color_prompt" = yes ]; then PS1='${debian_chroot:+($debian_chroot)}[\033[01;32m]\u@\h[\033[00m]:[\033[01;34m]\w[\033[00m]\$ ' else PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ ' fi unset color_prompt force_color_prompt

If this is an xterm set the title to user@host:dir

case "$TERM" in xterm|rxvt) PS1="[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a]$PS1" ;; *) ;; esac

enable color support of ls and also add handy aliases

if [ -x /usr/bin/dircolors ]; then test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)" alias ls='ls --color=auto'

alias dir='dir --color=auto'

#alias vdir='vdir --color=auto'

alias grep='grep --color=auto'
alias fgrep='fgrep --color=auto'
alias egrep='egrep --color=auto'

fi

colored GCC warnings and errors

export GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'

some more ls aliases

alias ll='ls -alF' alias la='ls -A' alias l='ls -CF'

Add an "alert" alias for long running commands. Use like so:

sleep 10; alert

alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal || echo error)" "$(history|tail -n1|sed -e '\''s/^\s[0-9]+\s//;s/[;&|]\s*alert$//'\'')"'

Alias definitions.

You may want to put all your additions into a separate file like

~/.bash_aliases, instead of adding them here directly.

See /usr/share/doc/bash-doc/examples in the bash-doc package.

if [ -f ~/.bash_aliases ]; then . ~/.bash_aliases fi

enable programmable completion features (you don't need to enable

this, if it's already enabled in /etc/bash.bashrc and /etc/profile

sources /etc/bash.bashrc).

if ! shopt -oq posix; then if [ -f /usr/share/bash-completion/bash_completion ]; then . /usr/share/bash-completion/bash_completion elif [ -f /etc/bash_completion ]; then . /etc/bash_completion fi fi

>>> conda initialize >>>

!! Contents within this block are managed by 'conda init' !!

conda_setup="$('/home/d/anaconda3/envs/bactopia/bin/conda' 'shell.bash' 'hook' 2> /dev/null)" if [ $? -eq 0 ]; then eval "$__conda_setup" else if [ -f "/home/d/anaconda3/envs/bactopia/etc/profile.d/conda.sh" ]; then . "/home/d/anaconda3/envs/bactopia/etc/profile.d/conda.sh" else export PATH="/home/d/anaconda3/envs/bactopia/bin:$PATH" fi fi unset conda_setup

if [ -f "/home/d/anaconda3/envs/bactopia/etc/profile.d/mamba.sh" ]; then . "/home/d/anaconda3/envs/bactopia/etc/profile.d/mamba.sh" fi

<<< conda initialize <<<

alias benjamon='ssh bleyton@200.13.6.10' alias soro='ssh mdavid@200.13.6.10' alias activate_defensefinder='source defensefinder/bin/activate'
alias atenea='ssh -i atenea.pem ubuntu@137.205.69.156'

export PATH="/home/d/LS-BSR/blast/ncbi-blast-2.15.0+/bin:$PATH" export PATH="/home/d/samtools/htslib/tabix/bin:$PATH" export PATH="/home/d/minimap2/minimap2/bin:$PATH" export PATH="/home/d/samtools/htslib/bgzip/bin:$PATH"
export PATH="/home/d/samtools/bin:$PATH"

export BCFTOOLS_PLUGINS=/home/d/bcftools/plugins"

and this is the error that gives me:

I would be really grateful if you can help me. Im new at this so maybe im doing something very stupid. Thanks for reading this and sorry for my stupidity.

Cheers from Chile, south america